A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
This report has been generated by the nf-core/quantms analysis pipeline. For information about how to interpret these results, please see the documentation.
/home/runner/work/pmultiqc/pmultiqc/data
pmultiqc
pmultiqc is a MultiQC module to show the pipeline performance of mass spectrometry based quantification pipelines such as nf-core/quantms, MaxQuant, and DIA-NN.URL: https://github.com/bigbio/pmultiqc
Experiment Setup
Experimental Design
| Sample Name | MSstats Condition: CT | MSstats Condition: CN | MSstats Condition: QY | MSstats BioReplicate | Fraction Group | Fraction | Label |
|---|---|---|---|---|---|---|---|
| 1 | Mixture | UPS1 | 0.1fmol | 1 | |||
| 1 | 1 | 1 | |||||
| 2 | 1 | 1 | |||||
| 2 | Mixture | UPS1 | 0.25fmol | 2 | |||
| 3 | 1 | 1 | |||||
| 4 | 1 | 1 |
Summary and HeatMap
Summary Table
| #Peptides Quantified | #Proteins Quantified |
|---|---|
| 5729 | 1605 |
Pipeline Result Statistics
| Sample Name | MSstats Condition: CT | MSstats Condition: CN | MSstats Condition: QY | Fraction | #Peptide IDs | #Unambiguous Peptide IDs | #Modified Peptide IDs | #Protein (group) IDs |
|---|---|---|---|---|---|---|---|---|
| 1 | Mixture | UPS1 | 0.1fmol | |||||
| 1 | 5407 | 5407 | 871 | 1552 | ||||
| 1 | 5434 | 5434 | 880 | 1562 | ||||
| 2 | Mixture | UPS1 | 0.25fmol | |||||
| 1 | 5572 | 5572 | 901 | 1578 | ||||
| 1 | 5558 | 5558 | 896 | 1588 |
Identification Summary
Number of Peptides identified Per Protein
ProteinGroups Count
Peptide ID Count
Modifications Per Raw File
Quantification Analysis
Peptides Quantification Table
| PeptideID | Protein Name | Peptide Sequence | Best Search Score | Average Intensity | CT=Mixture;CN=UPS1;QY=0.1fmol | CT=Mixture;CN=UPS1;QY=0.25fmol |
|---|---|---|---|---|---|---|
| 1 | TOLA_ECOLI | AAAEADDIFGELSSGK | 1.0000 | 5.9278 | 5.8889 | 5.9636 |
| 2 | G3P2_ECOLI | AAAENIIPHTTGAAK | 1.0000 | 5.8269 | 5.7804 | 5.8688 |
| 3 | RLMH_ECOLI | AAAEQSWSLSALTLPHPLVR | 1.0000 | 6.2390 | 6.1953 | 6.2787 |
| 4 | PDXJ_ECOLI | AAAEVGAPFIEIHTGCYADAK | 0.9997 | 5.4008 | 5.4976 | 5.2760 |
| 5 | RL10_ECOLI | AAAFEGELIPASQIDR | 1.0000 | 8.2489 | 8.2045 | 8.2892 |
| 6 | YFGM_ECOLI | AAAQLQQGLADTSDENLK | 1.0000 | 6.3880 | 6.3969 | 6.3789 |
| 7 | YFGM_ECOLI | AAAQLQQGLADTSDENLKAVINLR | 1.0000 | 6.1712 | 6.0321 | 6.2764 |
| 8 | RHLE_ECOLI | AAATGEALSLVCVDEHK | 1.0000 | 5.7073 | 5.6799 | 5.7331 |
| 9 | SYP_ECOLI | AAATQEMTLVDTPNAK | 1.0000 | 6.2840 | 6.2035 | 6.3518 |
| 10 | EUTL_ECOLI | AACNAFTDAVLEIAR | 1.0000 | 5.6299 | 5.6044 | 5.6541 |
| 11 | ACRB_ECOLI | AADGQMVPFSAFSSSR | 1.0000 | 6.0764 | 5.9387 | 6.1808 |
| 12 | YIDA_ECOLI | AADGSTVAQTALSYDDYR | 0.9998 | 5.6988 | 5.6826 | 5.7144 |
| 13 | ADHE_ECOLI | AADIVLQAAIAAGAPK | 1.0000 | 7.3764 | 7.3461 | 7.4048 |
| 14 | NARG_ECOLI | AADLVDALGQENNPEWK | 1.0000 | 5.6929 | 5.6454 | 5.7357 |
| 15 | DNAK_ECOLI | AADNKSLGQFNLDGINPAPR | 0.9998 | 5.5334 | 5.4957 | 5.5510 |
| 16 | OXYR_ECOLI | AADSCHVSQPTLSGQIR | 1.0000 | 6.2817 | 6.2485 | 6.3126 |
| 17 | TALA_ECOLI | AAEELEKEGINCNLTLLFSFAQAR | 1.0000 | 6.2640 | 6.2059 | 6.3153 |
| 18 | HEMY_ECOLI | AAELAGNDTIPVEITR | 0.9999 | 6.4392 | 6.4256 | 6.4523 |
| 19 | SYL_ECOLI | AAENNPELAAFIDECR | 1.0000 | 6.6836 | 6.6402 | 6.7231 |
| 20 | TALB_ECOLI | AAEQLEKEGINCNLTLLFSFAQAR | 1.0000 | 6.9806 | 6.8963 | 7.0512 |
| 21 | MBHM_ECOLI | AAESALNIDVPVNAQYIR | 1.0000 | 6.1335 | 6.1304 | 6.1366 |
| 22 | DNAG_ECOLI | AAESGVSRPVPQLKR | 0.9999 | 5.1143 | 4.9585 | 5.2288 |
| 23 | HDFR_ECOLI | AAESLYLTQSAVSFR | 1.0000 | 5.7540 | 5.7105 | 5.7935 |
| 24 | RNE_ECOLI | AAESRPAPFLIHQESNVIVR | 1.0000 | 6.5752 | 6.5572 | 6.5925 |
| 25 | HFLK_ECOLI | AAFDDAIAARENEQQYIR | 1.0000 | 5.8013 | 5.6354 | 5.9210 |
| 26 | AROF_ECOLI | AAFPLSLQQEAQIADSR | 1.0000 | 5.9273 | 5.9306 | 5.9241 |
| 27 | AROF_ECOLI | AAFPLSLQQEAQIADSRK | 0.9998 | 5.7612 | 5.7318 | 5.7887 |
| 28 | BOLA_ECOLI | AAFQPVFLEVVDESYR | 1.0000 | 6.4279 | 6.4107 | 6.4444 |
| 29 | CLPB_ECOLI | AAGATTANITQAIEQMR | 1.0000 | 5.9836 | 5.9726 | 5.9908 |
| 30 | YBIS_ECOLI | AAGEPLPAVVPAGPDNPMGLYALYIGR | 1.0000 | 5.9628 | 5.8381 | 6.0596 |
| 31 | SDHA_ECOLI | AAGLHLQESIAEQGALR | 1.0000 | 5.4225 | 5.4295 | 5.4154 |
| 32 | TALA_ECOLI | AAGLSQYEHLIDDAIAWGK | 0.9998 | 5.1833 | 5.1162 | 5.2413 |
| 33 | TALA_ECOLI | AAGLSQYEHLIDDAIAWGKK | 1.0000 | 5.8222 | 5.7763 | 5.8638 |
| 34 | ADHE_ECOLI | AAGVETEVFFEVEADPTLSIVR | 1.0000 | 6.4683 | 6.5168 | 6.4137 |
| 35 | ADHE_ECOLI | AAGVETEVFFEVEADPTLSIVRK | 0.9998 | 6.8321 | 6.7758 | 6.8819 |
| 36 | ENO_ECOLI | AAGYELGKDITLAMDCAASEFYK | 1.0000 | 6.6467 | 6.6291 | 6.6636 |
| 37 | YEBE_ECOLI | AAHQDEPQFGAQSTPLDER | 0.9998 | 5.6491 | 5.6220 | 5.6746 |
| 38 | RIBB_ECOLI | AAIADGAKPSDLNRPGHVFPLR | 1.0000 | 6.4630 | 6.4313 | 6.4926 |
| 39 | DEOC_ECOLI | AAIAYGADEVDVVFPYR | 1.0000 | 6.7499 | 6.6917 | 6.8012 |
| 40 | IDH_ECOLI | AAIEYAIANDRDSVTLVHK | 1.0000 | 6.2872 | 6.2689 | 6.3048 |
| 41 | DPO1_ECOLI | AAINAPMQGTAADIIKR | 0.9998 | 5.8750 | 5.8517 | 5.8972 |
| 42 | SYFA_ECOLI | AAISQASDVAALDNVR | 1.0000 | 6.5821 | 6.5777 | 6.5864 |
| 43 | SYFA_ECOLI | AAISQASDVAALDNVRVEYLGK | 1.0000 | 6.0451 | 5.9836 | 6.0990 |
| 44 | MUKF_ECOLI | AAISSCELLLSETSGTLR | 0.9998 | 5.4539 | 5.3950 | 5.5057 |
| 45 | MSCM_ECOLI | AAKPAQPEVVEALQSALNALEER | 0.9999 | 5.2647 | 5.1693 | 5.3428 |
| 46 | AMPN_ECOLI | AALEQLKGLENLSGDLYEK | 1.0000 | 6.2583 | 6.1947 | 6.3138 |
| 47 | DBHA_ECOLI | AALESTLAAITESLK | 1.0000 | 7.0020 | 7.0119 | 6.9919 |
| 48 | HEM3_ECOLI | AALPPEISLPAVGQGAVGIECR | 0.9999 | 6.3107 | 6.2797 | 6.3396 |
| 49 | SDHA_ECOLI | AALQISQSGQTCALLSK | 0.9999 | 5.5633 | 5.4781 | 5.6344 |
| 50 | DHE4_ECOLI | AANAGGVATSGLEMAQNAAR | 1.0000 | 5.7321 | 5.6606 | 5.7934 |
Protein Quantification Table
| ProteinID | Protein Name | Number of Peptides | Average Intensity | CT=Mixture;CN=UPS1;QY=0.1fmol | CT=Mixture;CN=UPS1;QY=0.25fmol |
|---|---|---|---|---|---|
| 1 | 3PASE_ECOLI | 1 | 5.6235 | 5.6046 | 5.6415 |
| 2 | 5DNU_ECOLI | 1 | 5.1934 | 5.1118 | 5.2621 |
| 3 | 6PGD_ECOLI | 10 | 7.4306 | 7.4143 | 7.4446 |
| 4 | 6PGL_ECOLI | 2 | 6.5057 | 6.4721 | 6.5331 |
| 5 | AAEB_ECOLI | 1 | 6.1800 | 6.1410 | 6.2158 |
| 6 | AAS_ECOLI | 4 | 6.0912 | 6.0728 | 6.0645 |
| 7 | AAT_ECOLI | 2 | 7.1735 | 7.1515 | 7.1944 |
| 8 | ABGT_ECOLI | 1 | 5.2444 | 5.3301 | 5.1374 |
| 9 | ACCA_ECOLI | 10 | 7.5188 | 7.4724 | 7.5607 |
| 10 | ACCC_ECOLI | 11 | 7.5447 | 7.5080 | 7.5786 |
| 11 | ACCD_ECOLI | 4 | 6.9568 | 6.9438 | 6.9695 |
| 12 | ACEA_ECOLI | 10 | 7.0495 | 7.0004 | 7.0936 |
| 13 | ACFD_ECOLI | 8 | 6.8296 | 6.7905 | 6.8657 |
| 14 | ACKA_ECOLI | 9 | 8.1525 | 8.1204 | 8.1816 |
| 15 | ACNA_ECOLI | 5 | 6.1236 | 6.0315 | 6.1795 |
| 16 | ACNB_ECOLI | 11 | 7.4528 | 7.4149 | 7.4828 |
| 17 | ACRA_ECOLI | 6 | 7.4974 | 7.4509 | 7.5394 |
| 18 | ACRB_ECOLI | 6 | 6.7660 | 6.6959 | 6.8263 |
| 19 | ACSA_ECOLI | 2 | 5.6039 | 5.6355 | 5.5511 |
| 20 | ACUI_ECOLI | 5 | 7.0524 | 6.9583 | 7.1097 |
| 21 | ACYP_ECOLI | 1 | 5.6173 | 5.6039 | 5.6238 |
| 22 | ADD_ECOLI | 5 | 7.1199 | 7.1375 | 7.1068 |
| 23 | ADEC_ECOLI | 1 | 5.3880 | 5.3527 | 5.4207 |
| 24 | ADHE_ECOLI | 33 | 8.5391 | 8.4942 | 8.5798 |
| 25 | ADHP_ECOLI | 2 | 5.8313 | 5.8293 | 5.8333 |
| 26 | ADIA_ECOLI | 3 | 5.9251 | 5.8502 | 5.9848 |
| 27 | ADPP_ECOLI | 2 | 6.3923 | 6.3622 | 6.4204 |
| 28 | AGP_ECOLI | 3 | 6.1377 | 6.1064 | 6.1668 |
| 29 | AHPC_ECOLI | 9 | 7.9186 | 7.8892 | 7.9463 |
| 30 | AHPF_ECOLI | 9 | 7.4292 | 7.4037 | 7.4533 |
| 31 | AHR_ECOLI | 1 | 5.0382 | 5.1352 | 4.9801 |
| 32 | AK1H_ECOLI | 7 | 6.4884 | 6.4593 | 6.5158 |
| 33 | AK2H_ECOLI | 4 | 6.5019 | 6.4721 | 6.5298 |
| 34 | AK3_ECOLI | 5 | 6.6134 | 6.5366 | 6.6421 |
| 35 | ALAA_ECOLI | 3 | 6.6067 | 6.5814 | 6.6305 |
| 36 | ALAC_ECOLI | 5 | 6.4739 | 6.4394 | 6.5059 |
| 37 | ALDB_ECOLI | 1 | 6.0428 | 6.0105 | 6.0729 |
| 38 | ALF1_ECOLI | 2 | 5.7993 | 5.0883 | 5.8061 |
| 39 | ALF_ECOLI | 10 | 7.9717 | 7.9422 | 7.9992 |
| 40 | ALKH_ECOLI | 3 | 6.6459 | 6.5686 | 6.7115 |
| 41 | ALR1_ECOLI | 3 | 6.6652 | 6.6304 | 6.6974 |
| 42 | AMIA_ECOLI | 1 | 5.8082 | 5.7658 | 5.8469 |
| 43 | AMIB_ECOLI | 2 | 5.7290 | 5.6933 | 5.7621 |
| 44 | AMIC_ECOLI | 5 | 5.9764 | 5.8423 | 6.0306 |
| 45 | AMID_ECOLI | 1 | 4.6107 | 4.3583 | 4.6972 |
| 46 | AMN_ECOLI | 8 | 6.7648 | 6.7423 | 6.7877 |
| 47 | AMPA_ECOLI | 7 | 7.1145 | 7.0752 | 7.1505 |
| 48 | AMPC_ECOLI | 2 | 6.1201 | 6.0621 | 6.1713 |
| 49 | AMPH_ECOLI | 2 | 6.1563 | 6.0922 | 6.2121 |
| 50 | AMPN_ECOLI | 7 | 7.0764 | 7.0526 | 7.0991 |
Intensity Distribution
Standard Deviation of Intensity
MS2 and Spectral Stats
Charge-state of Per File
MS/MS Counts Per 3D-peak
Time and Mass Error Trends
IDs over RT
nf-core/quantms Software Versions
nf-core/quantms Software Versions are collected at run time from the software output.URL: https://github.com/nf-core/quantms
| Process Name | Software | Version |
|---|---|---|
| ASSEMBLE_EMPIRICAL_LIBRARY | DIA-NN | 1.8.1 |
| CUSTOM_DUMPSOFTWAREVERSIONS | python | 3.9.5 |
| yaml | 5.4.1 | |
| DIANNCFG | sdrf-pipelines | 0.0.21 |
| DIANNCONVERT | sdrf-pipelines | 0.0.21 |
| DIANNSUMMARY | DIA-NN | 1.8.1 |
| DIANN_PRELIMINARY_ANALYSIS | DIA-NN | 1.8.1 |
| INDIVIDUAL_FINAL_ANALYSIS | DIA-NN | 1.8.1 |
| MSSTATS | bioconductor-msstats | 4.2.0 |
| r-base | 4.1.2 | |
| SAMPLESHEET_CHECK | sdrf-pipelines | 0.0.21 |
| SDRFPARSING | sdrf-pipelines | 0.0.21 |
| THERMORAWFILEPARSER | ThermoRawFileParser | 1.3.4 |
| Workflow | Nextflow | 21.10.6 |
| nf-core/quantms | 1.1dev |
nf-core/quantms Workflow Summary
- this information is collected when the pipeline is started.URL: https://github.com/nf-core/quantms
Core Nextflow options
- runName
- voluminous_thompson
- containerEngine
- docker
- launchDir
- /home/chengxin/newPR/quantms
- workDir
- /home/chengxin/newPR/quantms/work
- projectDir
- /home/chengxin/newPR/quantms
- userName
- chengxin
- profile
- test_dia,docker
- configFiles
- /home/chengxin/newPR/quantms/nextflow.config
Input/output options
- input
- /home/chengxin/diatestdata/PXD026600/PXD026600Partial2.sdrf.tsv
- outdir
- ./results_dia
Protein database
- database
- /home/chengxin/diatestdata/PXD026600/REF_EColi_K12_UPS1_combined.fasta
Database search
- allowed_missed_cleavages
- 1
- instrument
- N/A
- max_precursor_charge
- 3
- min_peptide_length
- 15
- max_peptide_length
- 30
- max_mods
- 2
Modification localization
- luciphor_debug
- N/A
PSM re-scoring (general)
- run_fdr_cutoff
- 0.10
PSM re-scoring (Percolator)
- description_correct_features
- N/A
Consensus ID
- consensusid_considered_top_hits
- N/A
- min_consensus_support
- N/A
Isobaric analyzer
- select_activation
- HCD
Protein Quantification (DDA)
- ratios
- N/A
- normalize
- N/A
- fix_peptides
- N/A
DIA-NN
- acquisition_method
- N/A
- mass_acc_ms2
- 13
- mass_acc_ms1
- 7
- scan_window
- 8
- min_pr_mz
- 350
- max_pr_mz
- 950
- min_fr_mz
- 500
- max_fr_mz
- 1500
- diann_normalize
- N/A
Statistical post-processing
- contrasts
- pairwise
Quality control
- enable_pmultiqc
- true
Institutional config options
- config_profile_name
- Test profile for DIA
- config_profile_description
- Minimal test dataset to check pipeline function for the data-independent acquisition pipeline branch.
Max job request options
- max_cpus
- 2
- max_memory
- 6 GB
- max_time
- 2d
Generic options
- hostnames
- N/A